CSS Classes on Menu

Hi Guys,

I’m creating a wordpress theme for a school work.
I have created my own HTML/CSS with bootstrap outside of wordpress and now i’m converting my HTML/CSS template into wordpress but i’m having some problemas with my menu.

I have this code in functions.php to register the menu
register_nav_menu( 'primary', 'Primary Menu' );

Then i have my menu like this on header.php

<nav class="navbar navbar-inverse navbar-fixed-top header" role="navigation">
        <div class="container">
            <!-- Brand and toggle get grouped for better mobile display -->
            <div class="navbar-header">
                <button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1">
                    <span class="sr-only">Toggle navigation</span>
                    <span class="icon-bar"></span>
                    <span class="icon-bar"></span>
                    <span class="icon-bar"></span>
                </button>
                <a class="brand" href="<?php echo site_url(); ?>"><?php bloginfo('name'); ?></a>
            </div>

            <!-- Collect the nav links, forms, and other content for toggling -->
            <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
                <ul class="nav navbar-nav">
                  <?php wp_nav_menu( array( 'theme_location' => 'primary' ) ); ?>
            </div>
            <!-- /.navbar-collapse -->
        </div>
        <!-- /.container -->
    </nav>

The problem is:
When i choose my menu on wordpress dashboard the css classes that i have on my header are not working and wordpress are using weird classes when i use the inspector on firefox. Like this: http://prntscr.com/bf28lj

How is wordpress doing this? And how can i change that?
I work good with html/css but i’m a newbie in Javascript/PHP.